Mercurial > repos > artbio > sr_bowtie_dataset_annotation

annotate sr_bowtie_dataset_annotation.xml @ 3:990b37ae7d78 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
author artbio
date Mon, 11 Apr 2022 00:27:02 +0000
parents e6cba7203dbd
children 7e0dbc330dfc
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990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
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1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.7">
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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2 <description>by iterative alignments with sRbowtie</description>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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3 <requirements>
1
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4 <requirement type="package" version="1.3.1">bowtie</requirement>
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5 <requirement type="package" version="1.7.1">r-optparse</requirement>
19ba2e38e8ec "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 1010eff91c8ce7415d50adaf2f83ecc278295df8"
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6 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
19ba2e38e8ec "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 1010eff91c8ce7415d50adaf2f83ecc278295df8"
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7 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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8 </requirements>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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9 <command detect_errors="exit_code"><![CDATA[
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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10 #if $refGenomeSource1.genomeSource == "history":
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11 bowtie-build -f $refGenomeSource1.ownFile genome 1>/dev/null &&
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12 #set index_path = 'genome'
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13 #else:
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14 #set index_path = $refGenomeSource1.index.fields.path
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15 #end if
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16
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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17 #for $i in $AdditionalQueries:
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18 bowtie-build -f $i.ownFile $i.ownFile.name 1>/dev/null &&
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19 #end for
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20
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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21 #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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22 #if $input[0].is_of_type('fasta'):
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23 #set format = "-f"
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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24 #elif $input[0].is_of_type('fastq'):
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25 #set format = "-q"
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26 #end if
3
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27
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
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28 mkdir unmatched_dir &&
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
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29
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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30 #for $file in $input:
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31 #set sample=$file.element_identifier
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32 bowtie -p \${GALAXY_SLOTS:-4}
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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33 $method_prefix
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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34 --al matched.fa
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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35 --un unmatched.fa
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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36 --suppress 6,7,8
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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37 $index_path $format $file > tabular_bowtie_output.tab &&
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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38 genome_aligned=\$(wc -l < matched.fa) &&
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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39 genome_aligned=\$(( \$genome_aligned/2)) &&
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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40 #set counter = 0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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41 #for $i in $AdditionalQueries:
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42 #set $counter += 1
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43 #if $counter != 1:
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44 #set to_align = "class_unmatched.fa"
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45 #else:
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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46 #set to_align = "matched.fa"
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47 #end if
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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48 touch tmp_class_matched.fa tmp_class_unmatched.fa &&
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49 bowtie -p \${GALAXY_SLOTS:-4}
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50 $method_prefix
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51 --al tmp_class_matched.fa
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52 --un tmp_class_unmatched.fa
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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53 --suppress 6,7,8
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54 $i.ownFile.name $format '$to_align' > tabular_bowtie_output.tab &&
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55 class_aligned=\$(( \$(wc -l < tmp_class_matched.fa)/2)) &&
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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56 class_unaligned=\$(( \$(wc -l < tmp_class_unmatched.fa)/2)) &&
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57 echo -e "$sample\t$i.ownFile.name\t\$class_aligned\t\${genome_aligned}" >> $output &&
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58 mv tmp_class_unmatched.fa class_unmatched.fa &&
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59 rm tmp_class_matched.fa &&
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60 #end for
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61 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
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62 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
3
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63 cp class_unmatched.fa unmatched_dir/${sample}_unmatched.fasta &&
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64 #if $format == '-q':
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65 mv unmatched_dir/${sample}_unmatched.fasta unmatched_dir/${sample}_unmatched.fastq &&
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66 sed -n '1~4s/^@/>/p;2~4p' unmatched_dir/${sample}_unmatched.fastq > unmatched_dir/${sample}_unmatched.fasta &&
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
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67 rm unmatched_dir/${sample}_unmatched.fastq &&
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68 #end if
0
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69 #end for
3
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
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70 ls -la unmatched_dir &&
0
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71 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
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72 ]]></command>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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73 <inputs>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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74 <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
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75 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
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76 <option value="0">0</option>
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77 <option value="1" selected="true">1</option>
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78 <option value="2">2</option>
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79 <option value="3">3</option>
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80 </param>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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81 <!-- First bowtie index selection -->
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
82 <conditional name="refGenomeSource1">
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
83 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Bowtie Built-ins were indexed using default options">
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
84 <option value="indexed">Use a built-in index</option>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
85 <option value="history">Use one from the history</option>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
86 </param>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
87 <when value="indexed">
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
88 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator">
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
89 <options from_data_table="bowtie_indexes"/>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
90 </param>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
91 </when>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
92 <when value="history">
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
93 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
94 </when>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
95 </conditional>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
96 <!-- End of first bowtie index selection -->
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
97 <!-- other bowtie index selections from fasta in history (mandatory) -->
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
98 <repeat name="AdditionalQueries" title="Additional Alignment Step">
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
99 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
100 </repeat>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
101 <!-- End of other bowtie index selections -->
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
102 </inputs>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
103 <outputs>
3
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
104 <collection name="unmatched" type="list" format="fasta" label="Annotate smRNAs: Unmatched reads">
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
105 <discover_datasets pattern="__name_and_ext__" directory="unmatched_dir" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
106 </collection>
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
107 <data format="tabular" name="output" label="Cascade Annotation Analysis">
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
108 <actions>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
109 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
110 </actions>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
111 </data>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
112 <data name="barplot" format="pdf" label="barplot from ${on_string}" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
113 </outputs>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
114 <tests>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
115 <test>
3
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
116 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
117 <param name="genomeSource" value="history" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
118 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
119 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
120 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
121 <output name="output" ftype="tabular" file="multisample5_output.tab" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
122 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
123 <output_collection name="unmatched" type="list" count="5">
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
124 <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta"/>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
125 <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta"/>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
126 <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta"/>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
127 <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta"/>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
128 <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
129 </output_collection>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
130 </test>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
131 <test>
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
132 <param name="input" value ="sample1.fa" ftype="fasta" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
133 <param name="genomeSource" value="history" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
134 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
135 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
136 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
137 <output name="output" ftype="tabular" file="sample1_output.tab" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
138 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
3
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
139 <output_collection name="unmatched" type="list">
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
140 <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
141 </output_collection>
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
142 </test>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
143 <test>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
144 <param name="input" value ="sample.fastq" ftype="fastq" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
145 <param name="genomeSource" value="history" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
146 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
147 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
148 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
149 <output name="output" ftype="tabular" file="sample_output.tab" />
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
150 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
3
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
151 <output_collection name="unmatched" type="list">
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
152 <element name="sample.fastq_unmatched" file="unmatched_fastq.fa" ftype="fasta"/>
990b37ae7d78 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit c8f13ba73552ccf7db7c22859b7fdc6ad121cdf0"
artbio
parents: 2
diff changeset
153 </output_collection>
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
154 </test>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
155 </tests>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
156 <help>
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
157
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
158 **Introduction**
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
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diff changeset
159
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
diff changeset
160 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
artbio
parents:
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161 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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162
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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163 Here The sRbowtie wrapper specifically works with short reads FASTA or FASTQ inputs
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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164 (-v bowtie mode, with -k 1) which has to be clipped from adapter before alignment.
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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165
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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166 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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167
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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168
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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169 ------
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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170
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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171 **What it does**
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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172
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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173 .. class:: infomark
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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174
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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175 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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176 Read that aligned to the first reference are realigned to the second reference.
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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177 From this point, unaligned reads are taken as input for alignment to the third reference, etc.
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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178
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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179
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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180 Reads are Matched on DNA references (both strands) as fast as possible, without taking care of mapping issues
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181
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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182 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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183
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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184 unaligned reads at step N are used as input for sRbowtie at step N+1
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185
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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186 -----
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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187
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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188 **Input formats**
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189
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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190 .. class:: warningmark
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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191
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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192 *Reads must be clipped from their adapter and provided in a FASTA or FASTQ format*
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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193
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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194 -----
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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195
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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196 **OUTPUTS**
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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197
2
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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198 **- Annotation table in a tabular format**
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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199
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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200 **- Pie Charts of class abundances**
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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201
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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202 **- Unmatched reads in fasta format**
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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203
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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204 </help>
2
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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205
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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206 <citations>
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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207 <citation type="doi">10.1038/nature11416</citation>
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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208 </citations>
e6cba7203dbd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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209
0
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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210 </tool>